This high-quality chromosome-level genome assembly of C. Saxicola will serve as a valuable resource for understanding the ecology, genetics, and evolution of the endangered herbaceous plant and will help towards its cultivation.
Abstract
Corydalis saxicola
, an endangered herbaceous plant belonging to the Papaveraceae family and used traditionally as folk medicine, is exclusively endemic to karst habitats. However, the lack of a reference genome limits the implementation of molecular techniques in its breeding, pharmacology and domestication. Here, we present a high-quality chromosome-level genome assembly of
C. saxicola
based on PacBio HiFi and Hi-C data. The assembled genome size is 240.94 Mb with a contig N50 of 29.21 Mb and BUSCO completeness of 97.71%. Approximately 93.26% of the assembled sequences could be anchored to eight pseudo-chromosomes. A total of 74.29 Mb repeat sequences were identified, which account for 32.33% of the genome. In addition, 24,203 protein-coding genes were identified with a BUSCO completeness of 97.89%. This high-quality genome assembly will serve as a valuable resource for understanding the ecology, genetics, and evolution of
C. Saxicola
and will help towards its cultivation.
This genome provides a foundational resource for investigating the molecular basis of evolutionary mechanisms, genetic breeding, and conservation genomics of male Andinoacara rivulatus, with direct implications for sustainable aquaculture and the global ornamental fish trade.
Zhen Yuan, Qi Liu, Hong-Wei Yan et al.· Scientific Data· 0 citations
Onychostoma lini
is an ecologically and economically important cyprinid species endemic to the mountain rivers of southern China. Wild populations have sharply declined due to habitat fragmentation, hydropower development, and overexploitation, yet genomic information remains unavailable, hindering studies on its diversity, adaptation, and conservation. Here, we assembled the first chromosome-level genome of
O. lini
using PacBio HiFi long-read sequencing, Illumina short-read polishing, and Hi-C scaffolding. The 907.5 Mb assembly achieved a contig N50 of 32.83 Mb and a scaffold N50 of 34.89 Mb, with 99.93% of sequences anchored to 25 chromosomes. Repetitive elements occupied 387.36 Mb, representing 42.69% of the genome. We predicted 28,597 protein-coding genes, 99.05% of which were functionally annotated in NR, KEGG, InterPro, SwissProt, and GO databases. BUSCO analysis identified 97.9% complete orthologs, confirming assembly completeness and annotation accuracy. This high-quality reference genome provides a foundational resource for investigating cyprinid evolution, environmental adaptation, and molecular breeding, and supports the conservation of
O. lini
.
Xuan Xie, Li Zou, Zhonggui Xie et al.· Scientific Data· 0 citations
Triosteum pinnatifidum
is a perennial herbaceous plant endemic to East Asia, whose roots, leaves, and fruits have long been utilized in traditional herbal medicine, thereby demonstrating substantial medicinal value. The root of
T. pinnatifidum
(commonly referred to as “Tianwangqi”) exhibits multiple pharmacological effects: enhancing Qi-blood circulation, dispelling wind-dampness, tonifying the spleen and stomach, and relieving inflammation and pain. However, the absence of a reference genome has impeded genetic research on this species. In the present study, we report a high-quality chromosome-level genome assembly of
T. pinnatifidum
generated using PacBio HiFi long-read sequencing and Hi-C scaffolding technologies. The final assembled genome spans 698.94 Mbp with a contig N50 of 46.55 Mbp, which was successfully anchored onto 9 chromosomes. Genome annotation revealed that repetitive sequences account for 65.84% of the genome, and a total of 26,027 protein-coding genes were predicted, among which 98.19% were functionally annotated. The final gene set of
T. pinnatifidum
exhibited a BUSCO completeness of 98.5%, indicating a high level of assembly accuracy and completeness. This genome assembly not only contributes to the genetic conservation of
Triosteum
L. species but also provides a valuable genomic resource for evolutionary studies within the Caprifoliaceae family.
Hai-Rui Liu, Huan Liu, Yao Wei et al.· Scientific Data· 0 citations
This chromosome-scale genome assembly and annotation of anise hyssop provides a foundational genomic resource for comparative and functional genomics within the genus Agastache and the Lamiaceae family.
Corallodiscus
is an oligotypic genus comprising five species, with
C. lanuginosus
being the most widespread distributed species and characterized by its extensive morphological variation, high genetic diversity, and ecological and medicinal significance as a resurrection plant. These features make it a valuable model for investigating taxonomy, genome evolution, and desiccation tolerance. However, genomic studies of this species have been limited by the absence of a high-quality reference genome. Here, we present a near-complete genome assembly of
C. lanuginosus
, representing the first genomic resource for the subtribe Corallodiscinae, generated using PacBio HiFi and Hi-C sequencing. The assembled genome spans 572.8 Mb, with a contig N50 of 41.0 Mb, and 555.9 Mb (97.1%) anchored onto ten pseudochromosomes. The assembly achieves high continuity and accurate, with a BUSCO completeness of 98.2%, a HiFi read mapping rate of 98.5%, an LAI of 24.7, and a QV of 53.8. A total of 20,600 protein-coding genes were predicted, of which 19,822 (96.2%) were functionally annotated. This high-quality genome provides a foundational resource for future studies on the evolutionary biology, adaptive mechanisms, and medicinally relevant traits of
Corallodiscus
.
Xi-Zuo Shi, Kun-Yue Ouyang, Li-Hua Yang et al.· Scientific Data· 0 citations
The Malabar red snapper (Lutjanus malabaricus) is a high-value marine food fish of growing economic and aquaculture importance across the Indo-Pacific. Despite its significance, genomic resources for this species have remained scarce, hindering the application of genomic tools for selective breeding. Here, we present the first chromosome-level genome assemblies and full-length transcriptome of L. malabaricus. Using PacBio HiFi long-read sequencing and Hi-C scaffolding, we generated high-quality assemblies for unsexed, male, and female individuals, each approximately 1.0 Gb in size and anchored to 24 chromosomes. The assemblies exhibited exceptional contiguity (N50 ≈ 42 Mb) and completeness (BUSCO > 99%), with karyotyping confirming 2n = 48 telocentric chromosomes. Genome annotation identified ~25,000 protein-coding genes, and repeat sequences accounted for almost half of the genome, comparable to other reef-associated teleosts. Comparative analyses of the male and female assemblies revealed strong chromosomal synteny and localized sex-associated regions, suggesting a polygenic or complex mechanism of sex determination. The accompanying multi-tissue full-length transcriptome supports functional and developmental studies. Together, these genomic and transcriptomic datasets provide a comprehensive molecular foundation for population genetics, comparative genomics, and selective breeding in L. malabaricus.
Shubha Vij, V. Nguyen, Kathiresan Purushothaman et al.· Scientific Data· 0 citations
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